molstar
Version:
A comprehensive macromolecular library.
60 lines (59 loc) • 2.6 kB
JavaScript
;
/**
* Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.getPositions = exports.getAtomIdForAtomRole = exports.getAtomicMoleculeType = exports.getElementMoleculeType = exports.getCoarseBegCompId = void 0;
var types_1 = require("./model/types");
var linear_algebra_1 = require("../../mol-math/linear-algebra");
function getCoarseBegCompId(unit, element) {
var entityKey = unit.coarseElements.entityKey[element];
var seq = unit.model.sequence.byEntityKey[entityKey].sequence;
var seq_id_begin = unit.coarseElements.seq_id_begin.value(element);
return seq.compId.value(seq_id_begin - 1); // 1-indexed
}
exports.getCoarseBegCompId = getCoarseBegCompId;
function getElementMoleculeType(unit, element) {
switch (unit.kind) {
case 0 /* Unit.Kind.Atomic */:
return unit.model.atomicHierarchy.derived.residue.moleculeType[unit.residueIndex[element]];
case 1 /* Unit.Kind.Spheres */:
case 2 /* Unit.Kind.Gaussians */:
// TODO add unit.model.coarseHierarchy.derived.residue.moleculeType
var compId = getCoarseBegCompId(unit, element);
var cc = unit.model.properties.chemicalComponentMap.get(compId);
if (cc)
return (0, types_1.getMoleculeType)(cc.type, compId);
}
return 0 /* MoleculeType.Unknown */;
}
exports.getElementMoleculeType = getElementMoleculeType;
function getAtomicMoleculeType(model, rI) {
return model.atomicHierarchy.derived.residue.moleculeType[rI];
}
exports.getAtomicMoleculeType = getAtomicMoleculeType;
var EmptyAtomIds = new Set();
function getAtomIdForAtomRole(polymerType, atomRole) {
var p = types_1.PolymerTypeAtomRoleId[polymerType];
if (p !== undefined) {
var a = p[atomRole];
if (a !== undefined)
return a;
}
return EmptyAtomIds;
}
exports.getAtomIdForAtomRole = getAtomIdForAtomRole;
var tmpPositionsVec = linear_algebra_1.Vec3.zero();
function getPositions(unit, indices) {
var pos = unit.conformation.position;
var positions = new Float32Array(indices.length * 3);
var elements = unit.elements;
for (var i = 0, il = indices.length; i < il; ++i) {
pos(elements[indices[i]], tmpPositionsVec);
linear_algebra_1.Vec3.toArray(tmpPositionsVec, positions, i * 3);
}
return positions;
}
exports.getPositions = getPositions;